Rebecca Greenblatt
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/CNViz |
| git_branch: RELEASE_3_14 |
| git_last_commit: e13c459 |
| git_last_commit_date: 2021-10-26 13:08:39 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:21 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the CNViz package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNViz.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 359/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNViz 1.2.0 (landing page) Rebecca Greenblatt
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CNViz |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CNViz_1.2.0.tar.gz |
| StartedAt: 2022-04-12 17:36:54 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 17:43:24 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 389.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNViz.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CNViz_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CNViz.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNViz' version '1.2.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CNViz' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
launchCNViz: no visible global function definition for 'is'
launchCNViz: no visible binding for global variable 'gene'
launchCNViz: no visible binding for global variable 'mutation_id'
launchCNViz: no visible binding for global variable 'ref'
launchCNViz: no visible binding for global variable 'alt'
launchCNViz: no visible binding for global variable 'sampleNames'
launchCNViz : server: no visible binding for global variable 'gene'
launchCNViz : server: no visible binding for global variable 'weight'
launchCNViz : server: no visible binding for global variable
'mean_log2'
launchCNViz : server: no visible binding for global variable 's'
launchCNViz : server: no visible binding for global variable 'e'
launchCNViz : server: no visible binding for global variable 'cn'
launchCNViz : server: no visible binding for global variable
'total_weight'
launchCNViz : server: no visible binding for global variable 'loh'
launchCNViz : server: no visible binding for global variable 'chrom'
launchCNViz : server: no visible binding for global variable
'chr1_subplot'
launchCNViz : server: no visible binding for global variable
'chr2_subplot'
launchCNViz : server: no visible binding for global variable
'chr3_subplot'
launchCNViz : server: no visible binding for global variable
'chr4_subplot'
launchCNViz : server: no visible binding for global variable
'chr5_subplot'
launchCNViz : server: no visible binding for global variable
'chr6_subplot'
launchCNViz : server: no visible binding for global variable
'chr7_subplot'
launchCNViz : server: no visible binding for global variable
'chr8_subplot'
launchCNViz : server: no visible binding for global variable
'chr9_subplot'
launchCNViz : server: no visible binding for global variable
'chr10_subplot'
launchCNViz : server: no visible binding for global variable
'chr11_subplot'
launchCNViz : server: no visible binding for global variable
'chr12_subplot'
launchCNViz : server: no visible binding for global variable
'chr13_subplot'
launchCNViz : server: no visible binding for global variable
'chr14_subplot'
launchCNViz : server: no visible binding for global variable
'chr15_subplot'
launchCNViz : server: no visible binding for global variable
'chr16_subplot'
launchCNViz : server: no visible binding for global variable
'chr17_subplot'
launchCNViz : server: no visible binding for global variable
'chr18_subplot'
launchCNViz : server: no visible binding for global variable
'chr19_subplot'
launchCNViz : server: no visible binding for global variable
'chr20_subplot'
launchCNViz : server: no visible binding for global variable
'chr21_subplot'
launchCNViz : server: no visible binding for global variable
'chr22_subplot'
launchCNViz : server: no visible binding for global variable
'chrX_subplot'
launchCNViz : server: no visible binding for global variable
'chrY_subplot'
launchCNViz : server: no visible binding for global variable
'study_name'
launchCNViz : server: no visible binding for global variable
'hugoGeneSymbol'
launchCNViz : server: no visible binding for global variable 'Gain'
launchCNViz : server: no visible binding for global variable
'Amplification'
launchCNViz : server: no visible binding for global variable
'ShallowDeletion'
launchCNViz : server: no visible binding for global variable
'DeepDeletion'
launchCNViz : server : <anonymous>: no visible binding for global
variable 'loh'
Undefined global functions or variables:
Amplification DeepDeletion Gain ShallowDeletion alt chr10_subplot
chr11_subplot chr12_subplot chr13_subplot chr14_subplot chr15_subplot
chr16_subplot chr17_subplot chr18_subplot chr19_subplot chr1_subplot
chr20_subplot chr21_subplot chr22_subplot chr2_subplot chr3_subplot
chr4_subplot chr5_subplot chr6_subplot chr7_subplot chr8_subplot
chr9_subplot chrX_subplot chrY_subplot chrom cn e gene hugoGeneSymbol
is loh mean_log2 mutation_id ref s sampleNames study_name
total_weight weight
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/CNViz.Rcheck/00check.log'
for details.
CNViz.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CNViz_1.2.0.tar.gz && rm -rf CNViz.buildbin-libdir && mkdir CNViz.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNViz.buildbin-libdir CNViz_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CNViz_1.2.0.zip && rm CNViz_1.2.0.tar.gz CNViz_1.2.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 109k 100 109k 0 0 211k 0 --:--:-- --:--:-- --:--:-- 211k
100 109k 100 109k 0 0 211k 0 --:--:-- --:--:-- --:--:-- 211k
install for i386
* installing *source* package 'CNViz' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CNViz'
finding HTML links ... done
all_tcga2018_data html
cbio_studies html
cytoband_data html
gene_data html
launchCNViz html
meta_data html
probe_data html
segment_data html
variant_data html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CNViz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNViz' as CNViz_1.2.0.zip
* DONE (CNViz)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CNViz' successfully unpacked and MD5 sums checked
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CNViz.Rcheck/examples_i386/CNViz-Ex.timings
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CNViz.Rcheck/examples_x64/CNViz-Ex.timings
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